Researchers don’t yet know the identity of all of the proteins. Nor do they understand what the spectrum of proteins suggests. But they’re learning, thanks to tissue donated by cancer patients. At Vanderbilt University Medical Center, for example, David Carbone, M.D., Ph.D., is leading a “molecular fingerprinting” study of lung tumors.

“We’re trying to determine if we can identify patterns at the time of diagnosis that can predict how a tumor’s going to behave,” says Carbone, Harold L. Moses Professor of Cancer Research. “If you knew this tumor was going to respond to chemotherapy, then you might consider giving adjuvant chemotherapy after surgery.”

Similar studies of cancerous breast, prostate and rectal tissue are being conducted at Vanderbilt. They join dozens of studies underway around the world. There is some early evidence that such studies can have powerful predictive value.

A complex world

Just what is this new science of proteins? How did we get here, and how far and how fast can we go?

The importance of proteins as the basic building blocks of life has been appreciated for more than 150 years (see “The Power of Proteins”), but until recently, the characterization of these fascinating molecules was a slow and arduous process. A scientist could spend a career trying to isolate, identify and understand a single protein—out of the hundreds of thousands that make up the human “proteome.”

Then came the fruits of the genomic and computer revolutions—methods for cloning genetic material (the “DNA”) and mass producing large quantities of it; automation and miniaturization; and the ability to create and sift through huge “libraries” of data on genes and proteins.

The recent sequencing of the 35,000 or so genes that make up the human genome has created a vast pool of information from which scientists hope to fish out ways to prevent dementia, cure cancer, and perhaps even eliminate ancient afflictions of the developing world.

For example:

At the University of Virginia, Donald Hunt, Ph.D., and colleagues have identified peptides—fragments of proteins—that trigger the body’s immune system to kill melanoma (skin cancer) cells. This could lead to the development of an effective vaccine against the disease.

Researchers at Stanford University have created a microarray or glass slide containing thousands of molecules that can bind to antibodies in the blood. It’s being tested as a way to improve the diagnosis of autoimmune diseases like rheumatoid arthritis, in which the body’s immune system attacks its own tissues.

Scientists at Johns Hopkins University have developed a new blood test for malaria using mass spectrometry, a way of measuring and identifying proteins. The method could lead to improvements in early diagnosis and treatment of the disease, which kills more than a million people in equatorial countries every year.

An “electronic taste chip” has been developed at the University of Texas at Austin that mimics the ability of the human taste bud to rapidly detect proteins and other chemicals in environmental samples. One possible application: detection of biological or chemical weapons.

As tantalizing as these examples are, few scientists predict that the discovery and understanding of important proteins will be as straightforward as the decade-long effort it took to read our genetic script. That’s because the DNA is more like a guidebook than a blueprint.